Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens

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Pentz, Jennifer T.Umeå universitet,Institutionen för molekylärbiologi (Medicinska fakulteten),Peter Lind (author)

Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens

Article/chapterEnglish2021

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2021-08-05
Public Library of Science,2021
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LIBRIS-ID:oai:DiVA.org:umu-186725
https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-186725URI
https://doi.org/10.1371/journal.pgen.1009722DOI

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Language:English
Summary in:English

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Experimental evolution with microbes is often highly repeatable under identical conditions, suggesting the possibility to predict short-term evolution. However, it is not clear to what degree evolutionary forecasts can be extended to related species in non-identical environments, which would allow testing of general predictive models and fundamental biological assumptions. To develop an extended model system for evolutionary forecasting, we used previous data and models of the genotype-to-phenotype map from the wrinkly spreader system in Pseudomonas fluorescens SBW25 to make predictions of evolutionary outcomes on different biological levels for Pseudomonas protegens Pf-5. In addition to sequence divergence (78% amino acid and 81% nucleotide identity) for the genes targeted by mutations, these species also differ in the inability of Pf-5 to make cellulose, which is the main structural basis for the adaptive phenotype in SBW25. The experimental conditions were changed compared to the SBW25 system to test if forecasts were extendable to a non-identical environment. Forty-three mutants with increased ability to colonize the air-liquid interface were isolated, and the majority had reduced motility and was partly dependent on the Pel exopolysaccharide as a structural component. Most (38/43) mutations are expected to disrupt negative regulation of the same three diguanylate cyclases as in SBW25, with a smaller number of mutations in promoter regions, including an uncharacterized polysaccharide synthase operon. A mathematical model developed for SBW25 predicted the order of the three main pathways and the genes targeted by mutations, but differences in fitness between mutants and mutational biases also appear to influence outcomes. Mutated regions in proteins could be predicted in most cases (16/22), but parallelism at the nucleotide level was low and mutational hot spot sites were not conserved. This study demonstrates the potential of short-term evolutionary forecasting in experimental populations and provides testable predictions for evolutionary outcomes in other Pseudomonas species.

Subject headings and genre

NATURVETENSKAP Biologi Evolutionsbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Evolutionary Biology hsv//eng
NATURVETENSKAP Biologi Genetik hsv//swe
NATURAL SCIENCES Biological Sciences Genetics hsv//eng
NATURVETENSKAP Biologi Mikrobiologi hsv//swe
NATURAL SCIENCES Biological Sciences Microbiology hsv//eng

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Lind, Peter A.Umeå universitet,Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet)(Swepub:umu)peli0125 (author)
Umeå universitetInstitutionen för molekylärbiologi (Medicinska fakulteten) (creator_code:org_t)

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In:PLOS Genetics: Public Library of Science17:81553-73901553-7404

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Evolutionary Bio ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Genetics

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Microbiology

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By the university: Umeå University

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